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- PDB-6l88: Crystal structure of mineralocorticoid receptor ligand binding do... -

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Basic information

Entry
Database: PDB / ID: 6l88
TitleCrystal structure of mineralocorticoid receptor ligand binding domain in complex with esaxerenone
ComponentsMineralocorticoid receptor
KeywordsTRANSCRIPTION / Nuclear receptor / Hypertension / NUCLEAR PROTEIN
Function / homology
Function and homology information


nuclear steroid receptor activity / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / nuclear receptor activity ...nuclear steroid receptor activity / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / nuclear receptor activity / sequence-specific double-stranded DNA binding / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / chromatin / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / signal transduction / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Chem-E6R / Mineralocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTakahashi, M. / Hanzawa, H.
CitationJournal: Febs Lett. / Year: 2020
Title: Crystal structure of the mineralocorticoid receptor ligand-binding domain in complex with a potent and selective nonsteroidal blocker, esaxerenone (CS-3150).
Authors: Takahashi, M. / Ubukata, O. / Homma, T. / Asoh, Y. / Honzumi, M. / Hayashi, N. / Saito, K. / Tsuruoka, H. / Aoki, K. / Hanzawa, H.
History
DepositionNov 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mineralocorticoid receptor
B: Mineralocorticoid receptor
C: Mineralocorticoid receptor
D: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,5058
Polymers116,6394
Non-polymers1,8664
Water00
1
A: Mineralocorticoid receptor
D: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2524
Polymers58,3192
Non-polymers9332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mineralocorticoid receptor
C: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2524
Polymers58,3192
Non-polymers9332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.888, 160.888, 160.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 983
2111B1 - 983
3111C1 - 983
4111D1 - 983

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.056718, 0.99839, 0.001081), (-0.039075, -0.003301, 0.999231), (0.997625, 0.056633, 0.0392)83.224358, 5.08728, -79.842621
3given(0.014944, 0.998745, 0.047794), (0.040083, 0.047162, -0.998083), (-0.999085, 0.016831, -0.039328)77.713432, -3.20728, 78.626678
4given(0.998036, 0.032591, 0.053494), (0.033054, -0.999423, -0.007786), (0.053209, 0.009539, -0.998538)0.27164, -0.89865, -5.78426

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Components

#1: Protein
Mineralocorticoid receptor / MR / Nuclear receptor subfamily 3 group C member 2


Mass: 29159.680 Da / Num. of mol.: 4 / Mutation: C808S,C910S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C2, MCR, MLR / Production host: Escherichia coli (E. coli) / References: UniProt: P08235
#2: Chemical
ChemComp-E6R / 1-(2-hydroxyethyl)-4-methyl-N-(4-methylsulfonylphenyl)-5-[2-(trifluoromethyl)phenyl]pyrrole-3-carboxamide / esaxerenone


Mass: 466.473 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H21F3N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist, hormone*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.0-2.5 M sodium nitrate, 0.1 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→19.96 Å / Num. obs: 27958 / % possible obs: 99.8 % / Redundancy: 10.303 % / Biso Wilson estimate: 93.301 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.397 / Rrim(I) all: 0.417 / Χ2: 1.053 / Net I/σ(I): 5.42 / Num. measured all: 552224
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.199.2586.610.3479609862185990.1017.00199.7
3.19-3.49.6544.5460.5378790816981610.2564.80199.9
3.4-3.6810.8342.531181882757175580.522.65799.8
3.68-4.0210.9381.3121.9576191697269660.7371.37799.9
4.02-4.510.9010.6224.2168961633963260.9170.65299.8
4.5-5.1810.4950.396.8158353556455600.9620.4199.9
5.18-6.339.6780.3646.945488470247000.9590.385100
6.33-8.8810.9220.11618.0439974366036600.9980.121100
8.88-19.9611.1160.03648.06229762096206710.03898.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mwp

5mwp


Resolution: 3→19.96 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.92 / SU B: 37.834 / SU ML: 0.612 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.696 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1441 5.2 %RANDOM
Rwork0.2685 ---
obs0.2705 26335 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 318.22 Å2 / Biso mean: 116.551 Å2 / Biso min: 52.77 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 128 0 6212
Biso mean--136.55 --
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136343
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176005
X-RAY DIFFRACTIONr_angle_refined_deg1.611.6378568
X-RAY DIFFRACTIONr_angle_other_deg1.1731.57313914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5385737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62122.951288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.48151169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3111528
X-RAY DIFFRACTIONr_chiral_restr0.0620.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026739
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021289
Refine LS restraints NCS

Ens-ID: 1 / Number: 2921 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A17.67
2B17.37
3C16.85
4D14.95
LS refinement shellResolution: 3.004→3.163 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.437 229 -
Rwork0.397 3671 -
all-3900 -
obs--98.88 %

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